Simple Summary: Significant progress has been made to understand shade and low-light due to their deteriorative impact on plant growth and crop yield. The authors of the present study identified novel microRNA (miR) regulations for tolerant phenotypic responses associated with a sustainable yield of Swarnaprabha, a shade-tolerant rice genotype. We present three new findings, two of which are demonstrations of novel concepts. First, we show that the differentially expressed miRs had drastic differences in the category of targets based on their function and pathway. Second, we show that neutrally regulated and uniquely expressed miRs can also contribute to the shade-tolerance response by altering the differential expression of their targets under different light conditions. Third, we identified the interactions of 16 miRNA and 21 target pairs, whose actions can significantly contribute to the shade-tolerance phenotype and sustainable yield of Swarnaprabha rice. The findings of this study will significantly update the knowledge of the epigenetic regulations of shade tolerance in rice. The authors of further studies can use the genomic data and findings of this study to generate shade-tolerant crop varieties to combat prevailing unpredictable weather conditions in order to maintain food security. Prolonged shade during the reproductive stage can result in significant yield losses in rice. For this study, we elucidated the role of microRNAs in prolonged-shade tolerance (~20 days of shade) in a shade-tolerant rice variety, Swarnaprabha (SP), in its reproductive stage using small RNA and degradome sequencing with expression analysis using microarray and qRT-PCR. This study demonstrates that miRNA (miR) regulation for shade-tolerance predominately comprises the deactivation of the miR itself, leading to the upregulation of their targets. Up- and downregulated differentially expressed miRs (DEms) presented drastic differences in the category of targets based on the function and pathway in which they are involved. Moreover, neutrally regulated and uniquely expressed miRs also contributed to the shade-tolerance response by altering the differential expression of their targets, probably due to their differential binding affinities. The upregulated DEms mostly targeted the cell wall, membrane, cytoskeleton, and cellulose synthesis-related transcripts, and the downregulated DEms targeted the transcripts of photosynthesis, carbon and sugar metabolism, energy metabolism, and amino acid and protein metabolism. We identified 16 miRNAs with 21 target pairs, whose actions may significantly contribute to the shade-tolerance phenotype and sustainable yield of SP. The most notable among these were found to be miR5493-OsSLAC and miR5144-OsLOG1 for enhanced panicle size, miR5493-OsBRITTLE1-1 for grain formation, miR6245-OsCsIF9 for decreased stem mechanical strength, miR5487-OsGns9 and miR168b-OsCP1 for better pollen development, and miR172b-OsbHLH153 for hyponasty under shade. [ABSTRACT FROM AUTHOR]